ABSTRACT
Introduction: Porcine epidemic diarrhoea virus (PEDV) is an enteric pathogen causing porcine epidemic diarrhoea and acute gastroenteritis in pigs of all ages. Previous analysis of the viral genome of PEDV in Poland was only based on the spike protein (S) gene sequences and no analysis of other genes has been performed. The aim of this study was to analyse the envelope (E), membrane (M) and nucleocapsid (N) protein and open reading frame 3 (ORF3) gene sequences. Material and Methods: Viral RNA from 18 Polish pig faecal samples that were quantitative reverse transcription PCR-positive for PEDV was analysed in four genomic regions (E, M, N and ORF3). Results: Phylogenetic analysis based on these regions' sequences revealed that Polish PEDV isolates were highly related and were clustered into group G2a across the four genes compared. Moreover, the Polish strains were located in distinct subclusters on the phylogenetic trees, which suggests the presence of at least three independently evolving PEDV genetic lines circulating in Poland. The occurrence of unique mutations in the sequences of Polish PEDV strains suggests that PEDV continues to undergo evolutionary processes, accumulating the mutations necessary for viral fitness in its natural hosts. The Polish PEDV strains differed genetically from the CV777 vaccine strain, suggesting the risk of relatively low vaccine efficacy if this strain is used. Conclusion: Our results promote a better understanding of the genetic diversity of PEDV field isolates in Poland and highlight the importance of molecular characterisation of PEDV field strains for the development of an effective vaccine against PEDV.
ABSTRACT
Method named as variant approach to recognizing genus of coronavirus that is based on frequency of codon distribution in viral ORF1ab and genes of structural proteins (S, M and N) was proposed in the work. This method uses modified statistics whose efficiency was demonstrated earlier for flavivirus species recognition. To recognize genus of coronavirus the variant approach considers both various combinations of several structural coronavirus genes and individual structural genes. Finally, coronavirus genus is determined in the result of analysis of all variants considered. The method proposed was developed with the help of learning sample from prototype viral variants of Alphacoronavirus, Betacoronavirus, Deltacoronavirus and Gammacoronavirus genus. Application of the variant approach to recognizing genus of coronavirus has demonstrated the approach high assurance at level of 95 %. Among all variants of joint analysis, the most reliability (98 %) in recognizing genus has been achieved if codon frequency of the ORF1ab was used. Variant approach has revealed a phenomenon of mosaic structure in coronavirus genomes, i.e., when the results of genus recognition for a few genes differ from final conclusion about coronavirus genus. It seems that such phenomenon reflects homologous recombinations of the genes between various species of the coronaviruses and plasticity of their genomes in evolutionary processes. © 2022. Mathematical Biology and Bioinformatics. All Rights Reserved.